Scaling, pixels, and aspect ratios are a particular area where I've experimented quite a bit. If I am trying to make a lower-resolution pixel-style game, the resolution I go for is...
640 x 360
Whenever you scale up a given resolution, you will get the best results if it scales evenly by integer values with the native resolution of whatever screen you are displaying it on. This is the best approach for preventing visual errors that occur due to native resolution adaptation. 640 x 360 is my favored resolution because it scales evenly by most of the industry-standard display resolutions. It is also the same 16x9 aspect ratio as most modern screens as well, so using it helps to avoid letterboxing. It will integer scale properly on a 720p screen, a 1080p screen, and even a 4K screen.
It is slightly higher resolution than most older consoles, but not so much that you lose the pixel-art effect. And it is very close to older PC monitors, so capturing the look of older PC games is quite easy with this resolution.